Help with uploading

This is the single entry point for user-supplied data. All files that contain information intended for import need to be uploaded here. To upload files, click the upload button and browse your local file system. You can select and upload multiple files at once by pressing [CTRL]. Currently, the following file types are supported:

Tabular data:

• .csv (comma-separated)
• .txt, .tsv (tab-separated)
• .xls, .xslx

Turboveg 2:

• xml

Veg-X:

• xml

If an upload of tabular data fails, check the following possible reasons or fixes:

• Column names are expected in the first line and their number must match the number of columns.
• If you have a text file and commas as column separators, use '.csv' as file extension. In case of tabs use '.tsv' or '.txt'.
• Space is currently not recognized as a delimiter.

Completed uploads are listed under 'Uploaded Files' with a corresponding icon for the file type.

Clicking on one of the file icons under 'Uploaded files' will activate the 'File Editor'. Depending on the file type, this may either be a text editor (for xml data) or a spreadsheet editor (for tabular data). Click on the 'Edit' tab above the data view to access functions for editing and reshaping the uploaded files.

Help with editing

Basic table editing can be reached using the context menu (right click on a column or row name when the table is in editing mode). The options are self-explanatory.

There is currently a bug in the underlying packages that prevents the table from being saved after removing scattered columns. You can work around this by first saving the object under a new name and then removing separated individual columns or blocks of columns one by one. Save the object after each removal.

More tools are available via the buttons at the top:

Help with reading tabular data

Check out the video tutorial on the entry page!

While the import from Turboveg is a one step procedure, tabular data comes in many flavours so that VegXshiny needs to be told which columns of a data table goes in which Veg-X container. The import dialogue guides through this procedure.

Importing requires the data to be organized so that each variable has its own column and each plot or observation has its own row. There should be only one column for each type of variable. For example, if you measured species cover, you need one column for species covers, another column for the respective species, and columns for plot IDs, dates and maybe vegetation layers. A date is only needed for time-dependent observations. The 'File editor' in the Upload section provided tools for transforming the data accordingly.

The import of tabular data is structured into five steps:

1. Project information

Provide a general description of the project and its contributors. No files need to be assigned in this step.

2. Plot information

Describe static plot properties (like surface area of the plot. This is distinguished from features that belong to a plotObservation, such as the date of a recording). The expected data set contains one plot per row. Each row is identified by a unique plot ID (mandatory).

Each mapped plot property needs to be linked to a measurement method. Prefabricated descriptions of common measurement methods are available in the corresponding mapping dialog. For example, if plot area was measured in square metres, selecting "Plot area/m2" as measurement method will define an appropriate method and link it to the measurement values during import. If none of the predefined methods is applicable, a custom method can be defined by selecting the "...add custom method" option.

3. Observations

Add time-dependent observations, such as species cover, vegetation layers, or soil properties. All observations in Veg-X refer to a plotObservation, i.e. a sampling event at a specific plot at a specific point in time. Observation data of any type are identified at least by a unique combination of plot ID and date .

As in the case of plot properties, measurements during observations require defined measurement methods. A dropdown menu provides a list of predefined methods. If none of these predefined methods is applicable, a custom method can be created by selecting the "...add custom method" option.

Note that currently VegXshiny does not support imports into the Veg-X container for measurements applying to an entire plant community, such as successional stage (called communityObservations). The same applies to measurements related to individual organisms, such as DBH (called individualOrganismObservations).

4. Check inputs

Check your mapped inputs before starting the import. Color-coded boxes indicate the status:

• Green : Inputs complete, ready for import.
• Red : Inputs incomplete, review before import.
• Grey : Inputs incomplete, ignored during import.

Only when all input categories are marked either green or grey, you will be able to proceed with the import.

5. Import

Pressing Import and confirming the dialog will create a new Veg-X document from the specified mappings. Your current Veg-X document will be overwritten by this.

Note that the import may take a while when working with large input files. A progress bar in the lower left corner indicates the current status. Once the import is finished, you can review the imported Veg-X file in the Review Section or export it under Download.

Help with importing Turboveg

You can import data from Turboveg 2 standard XML files .

Choose an uploaded Turboveg 2 XML file and press the read button. Once the extraction is finished, a summary is displayed.

Read Turboveg file, review the summary and run the import. The Import button will open a dialog where you can select, which 'undefined' Turboveg header data you want to import (i.e. data lacking information that is required by pre-defined Veg-X elements). The selected fields will be attached as user-defined to their corresponding plot node in the Veg-X document. Pressing Proceed will then start the conversion to Veg-X.

Help with reading Veg-X

Read Veg-X, review the summary and run the import.

Help with reviewing Veg-X

Typically, no action is required here and you can continue with the download.

You can edit the data after pressing the 'Edit' button but caution is advised, as manually editing a Veg-X document can quickly invalidate it. Note that edits cannot be undone once saved.

Pressing the 'Validate' button tests whether the current Veg-X document conforms to the Veg-X XML Schema and whether there are any potential problems with references to nodes. Validation errors and other problems are listed in the action log.

Help with downloading

If a valid Veg-X document is available, an overview of the structure (with the number of nodes of different types) is shown on this page. The Veg-X document can then be downloaded as:

• xml : Veg-X xml file
• zip : Set of 'long tables' - a format that can be easily processed by generic database systems. While these tables are provided as a zip archive of csv files, the same tables can also be downloaded as elements of an R list object:
• rds : R list object. Use readRDS() to read it into R.
• csv : A comma-separated 'wide table' or 'vegetation table') for import into spreadsheet programs.

Note that Turboveg 3 is able to import Veg-X XML documents.

Help with the action log

The Action Log records user actions and application messages during a session. This includes file uploads and edits, import messages, Veg-X document edits and validations and file exports. If any problem occurrs during the session, the Action Log may provide relevant information.